| Number of LoF | Affected | Control | Fisher |
|---|---|---|---|
| Grouping Method: Frequency | |||
| Rare variants | |||
| [25,48) | 20.000 | 66.000 | 0.125 |
| [48,92] | 28.000 | 53.000 | |
| [25,48) | 0.417 | 0.555 | |
| [48,92] | 0.583 | 0.445 | |
| Singletons | |||
| [0, 8) | 24.000 | 67.000 | 0.495 |
| [8,17] | 24.000 | 52.000 | |
| [0, 8) | 0.500 | 0.563 | |
| [8,17] | 0.500 | 0.437 | |
| Grouping Method: Presence versus Absence | |||
| Rare variants | |||
| 0 | 0.000 | 0.000 | 1 |
| [ 1,92] | 48.000 | 119.000 | |
| 0 | 0.000 | 0.000 | |
| [ 1,92] | 1.000 | 1.000 | |
| Singletons | |||
| 0 | 0.000 | 1.000 | |
| [ 1,92] | 48.000 | 118.000 | |
| 0 | 0.000 | 0.008 | |
| [ 1,92] | 1.000 | 0.992 | |
| Grouping Method: Kmeans | |||
| Rare variants | |||
| [25.0,52.6) | 29.000 | 87.000 | 0.137 |
| [52.6,92.0] | 19.000 | 32.000 | |
| [25.0,52.6) | 0.604 | 0.731 | |
| [52.6,92.0] | 0.396 | 0.269 | |
| Singletons | |||
| [ 0.00, 8.47) | 29.000 | 87.000 | |
| [ 8.47,17.00] | 19.000 | 32.000 | |
| [ 0.00, 8.47) | 0.604 | 0.731 | |
| [ 8.47,17.00] | 0.396 | 0.269 | |
| term | estimate | p.value |
|---|---|---|
| (Intercept) | -1386.014 | 0.996 |
| fra_fr1 | -39.094 | 0.994 |
| spl_fr4 | 110.454 | 0.995 |
| sto_fr2 | -43.300 | 0.995 |
| sto_fr3 | -25.312 | 0.995 |
| nfr_fr1 | 17.541 | 0.994 |
| nfr_fr2 | -43.654 | 0.995 |
| nfr_fr3 | -38.630 | 0.994 |
| nfr_fr4 | 169.998 | 0.995 |
| nsy_fr1 | 1.794 | 0.995 |
| syn_fr1 | -1.408 | 0.996 |
| syn_fr3 | 4.300 | 0.994 |
| syn_fr4 | -9.714 | 0.996 |
| utr5_fr3 | 10.648 | 0.996 |
| utr3_fr1 | 0.064 | 0.995 |
| utr3_fr3 | -3.969 | 0.994 |
| ncRNA_fr4 | 68.261 | 0.994 |
| miRNA_fr1 | 37.627 | 0.996 |
| miRNA_fr2 | 78.987 | 0.996 |
| miRNA_fr3 | 190.749 | 0.994 |
| miRNA_fr4 | -420.030 | 0.998 |
| bnd_fr2 | -1.306 | 0.996 |
| reg_fr2 | 19.270 | 0.996 |
| reg_fr3 | 33.597 | 0.994 |
| H | AUC | KS | TP | FP | TN | FN | |
|---|---|---|---|---|---|---|---|
| scores | 0.014 | 0.548 | 0.106 | 9 | 20 | 42 | 12 |
##
## Classification tree:
## rpart(formula = fml, data = lrn)
##
## Variables actually used in tree construction:
## [1] bnd_fr1 ncRNA_fr3 utr3_fr3
##
## Root node error: 27/84 = 0.32143
##
## n= 84
##
## CP nsplit rel error xerror xstd
## 1 0.22222 0 1.00000 1.0000 0.15853
## 2 0.11111 2 0.55556 1.0741 0.16139
## 3 0.01000 4 0.33333 1.1481 0.16380
| H | AUC | KS | TP | FP | TN | FN | |
|---|---|---|---|---|---|---|---|
| scores | 0.299 | 0.764 | 0.412 | 10 | 4 | 58 | 11 |
| H | AUC | KS | TP | FP | TN | FN | |
|---|---|---|---|---|---|---|---|
| V1 | 0 | 0.5 | 0 | 0 | 0 | 62 | 21 |
| H | AUC | KS | TP | FP | TN | FN | |
|---|---|---|---|---|---|---|---|
| scores | 0.224 | 0.71 | 0.343 | 2 | 0 | 62 | 19 |
## VCF Format ==> SNP GDS Format
## Method: exacting biallelic SNPs
## Number of samples: 179
## Parsing "ind179.vcf" ...
## import 1213997 variants.
## + genotype { Bit2 179x1213997, 51.8M } *
## Optimize the access efficiency ...
## Clean up the fragments of GDS file:
## open the file 'final.gds' (60.9M)
## # of fragments: 220
## save to 'final.gds.tmp'
## rename 'final.gds.tmp' (60.9M, reduced: 2.3K)
## # of fragments: 20
## Principal Component Analysis (PCA) on genotypes:
## Excluding 26,624 SNPs on non-autosomes
## Excluding 3,634 SNPs (monomorphic: TRUE, < MAF: NaN, or > missing rate: NaN)
## Working space: 179 samples, 1,183,739 SNPs
## using 1 (CPU) core
## PCA: the sum of all selected genotypes (0, 1 and 2) = 344168751
## Wed Jan 31 21:04:55 2018 (internal increment: 4184)
##
[..................................................] 0%, ETC: ---
[======================>...........................] 43%, ETC: 6s
[==============================================>...] 91%, ETC: 1s
[==================================================] 100%, completed
## Wed Jan 31 21:05:05 2018 Begin (eigenvalues and eigenvectors)
## Wed Jan 31 21:05:05 2018 Done.
| Number of LoF | Affected | Control | Fisher |
|---|---|---|---|
| Grouping Method: Frequency | |||
| Rare variants | |||
| [25,46) | 19.000 | 50.000 | 1 |
| [46,92] | 19.000 | 47.000 | |
| [25,46) | 0.500 | 0.515 | |
| [46,92] | 0.500 | 0.485 | |
| Singletons | |||
| [0, 8) | 20.000 | 52.000 | |
| [8,17] | 18.000 | 45.000 | |
| [0, 8) | 0.526 | 0.536 | |
| [8,17] | 0.474 | 0.464 | |
| Grouping Method: Presence versus Absence | |||
| Rare variants | |||
| 0 | 0.000 | 0.000 | |
| [ 1,92] | 38.000 | 97.000 | |
| 0 | 0.000 | 0.000 | |
| [ 1,92] | 1.000 | 1.000 | |
| Singletons | |||
| 0 | 0.000 | 1.000 | |
| [ 1,92] | 38.000 | 96.000 | |
| 0 | 0.000 | 0.010 | |
| [ 1,92] | 1.000 | 0.990 | |
| Grouping Method: Kmeans | |||
| Rare variants | |||
| [25.0,46.8) | 20.000 | 56.000 | 0.7 |
| [46.8,92.0] | 18.000 | 41.000 | |
| [25.0,46.8) | 0.526 | 0.577 | |
| [46.8,92.0] | 0.474 | 0.423 | |
| Singletons | |||
| [ 0.00, 7.64) | 20.000 | 52.000 | 1 |
| [ 7.64,17.00] | 18.000 | 45.000 | |
| [ 0.00, 7.64) | 0.526 | 0.536 | |
| [ 7.64,17.00] | 0.474 | 0.464 | |
| term | estimate | p.value |
|---|---|---|
| (Intercept) | -1143.488 | 0.997 |
| spl_fr1 | -9.677 | 0.996 |
| syn_fr1 | -0.296 | 0.996 |
| syn_fr2 | -1.978 | 0.996 |
| utr5_fr2 | 13.069 | 0.996 |
| ncRNA_fr1 | 0.865 | 0.996 |
| ncRNA_fr3 | 9.111 | 0.996 |
| bnd_fr3 | -2.706 | 0.996 |
| reg_fr1 | 3.444 | 0.996 |
| reg_fr2 | -20.612 | 0.997 |
| H | AUC | KS | TP | FP | TN | FN | |
|---|---|---|---|---|---|---|---|
| scores | 0.2 | 0.68 | 0.365 | 10 | 5 | 39 | 13 |
##
## Classification tree:
## rpart(formula = fml, data = lrn)
##
## Variables actually used in tree construction:
## [1] ncRNA_fr3 reg_fr4
##
## Root node error: 15/68 = 0.22058824
##
## n= 68
##
## CP nsplit rel error xerror xstd
## 1 0.20 0 1.0 1.0000000 0.22794908
## 2 0.01 2 0.6 1.3333333 0.25048972
| H | AUC | KS | TP | FP | TN | FN | |
|---|---|---|---|---|---|---|---|
| scores | 0.099 | 0.619 | 0.234 | 20 | 36 | 8 | 3 |
| H | AUC | KS | TP | FP | TN | FN | |
|---|---|---|---|---|---|---|---|
| V1 | 0 | 0.5 | 0 | 0 | 0 | 44 | 23 |
| H | AUC | KS | TP | FP | TN | FN | |
|---|---|---|---|---|---|---|---|
| scores | 0.475 | 0.801 | 0.605 | 0 | 0 | 44 | 23 |
| Number of LoF | Affected | Control | Fisher |
|---|---|---|---|
| Grouping Method: Frequency | |||
| Rare variants | |||
| [35,61) | 3.0 | 13.000 | 0.252 |
| [61,86] | 7.0 | 9.000 | |
| [35,61) | 0.3 | 0.591 | |
| [61,86] | 0.7 | 0.409 | |
| Singletons | |||
| [2, 9) | 4.0 | 15.000 | 0.244 |
| [9,13] | 6.0 | 7.000 | |
| [2, 9) | 0.4 | 0.682 | |
| [9,13] | 0.6 | 0.318 | |
| Grouping Method: Presence versus Absence | |||
| Rare variants | |||
| 0 | 0.0 | 0.000 | 1 |
| [ 1,86] | 10.0 | 22.000 | |
| 0 | 0.0 | 0.000 | |
| [ 1,86] | 1.0 | 1.000 | |
| Singletons | |||
| 0 | 0.0 | 0.000 | |
| [ 1,86] | 10.0 | 22.000 | |
| 0 | 0.0 | 0.000 | |
| [ 1,86] | 1.0 | 1.000 | |
| Grouping Method: Kmeans | |||
| Rare variants | |||
| [35.0,61.8) | 3.0 | 15.000 | 0.062 |
| [61.8,86.0] | 7.0 | 7.000 | |
| [35.0,61.8) | 0.3 | 0.682 | |
| [61.8,86.0] | 0.7 | 0.318 | |
| Singletons | |||
| [ 2.00, 7.85) | 4.0 | 15.000 | 0.244 |
| [ 7.85,13.00] | 6.0 | 7.000 | |
| [ 2.00, 7.85) | 0.4 | 0.682 | |
| [ 7.85,13.00] | 0.6 | 0.318 | |
| term | estimate | p.value |
|---|---|---|
| (Intercept) | 225.479 | 0.999 |
| fra_fr1 | -9.383 | 0.999 |
| spl_fr1 | 17.046 | 0.999 |
| spl_fr2 | -31.320 | 0.999 |
| sto_fr2 | -29.732 | 0.999 |
| nfr_fr3 | -13.087 | 0.999 |
| H | AUC | KS | TP | FP | TN | FN | |
|---|---|---|---|---|---|---|---|
| scores | 0.025 | 0.518 | 0.145 | 3 | 6 | 5 | 2 |
##
## Classification tree:
## rpart(formula = fml, data = lrn)
##
## Variables actually used in tree construction:
## character(0)
##
## Root node error: 5/16 = 0.3125
##
## n= 16
##
## CP nsplit rel error xerror xstd
## 1 0.01 0 1 0 0
| H | AUC | KS | TP | FP | TN | FN | |
|---|---|---|---|---|---|---|---|
| scores | 0 | 0.5 | 0 | 5 | 11 | 0 | 0 |
| H | AUC | KS | TP | FP | TN | FN | |
|---|---|---|---|---|---|---|---|
| V1 | 0 | 0.5 | 0 | 0 | 0 | 11 | 5 |
| H | AUC | KS | TP | FP | TN | FN | |
|---|---|---|---|---|---|---|---|
| scores | 0.276 | 0.673 | 0.364 | 0 | 0 | 11 | 5 |
| Number of LoF | Affected | Control | Fisher |
|---|---|---|---|
| Grouping Method: Frequency | |||
| Rare variants | |||
| [25,48) | 20.000 | 66.000 | 0.125 |
| [48,92] | 28.000 | 53.000 | |
| [25,48) | 0.417 | 0.555 | |
| [48,92] | 0.583 | 0.445 | |
| Singletons | |||
| [0, 8) | 24.000 | 67.000 | 0.495 |
| [8,17] | 24.000 | 52.000 | |
| [0, 8) | 0.500 | 0.563 | |
| [8,17] | 0.500 | 0.437 | |
| Grouping Method: Presence versus Absence | |||
| Rare variants | |||
| 0 | 0.000 | 0.000 | 1 |
| [ 1,92] | 48.000 | 119.000 | |
| 0 | 0.000 | 0.000 | |
| [ 1,92] | 1.000 | 1.000 | |
| Singletons | |||
| 0 | 0.000 | 1.000 | |
| [ 1,92] | 48.000 | 118.000 | |
| 0 | 0.000 | 0.008 | |
| [ 1,92] | 1.000 | 0.992 | |
| Grouping Method: Kmeans | |||
| Rare variants | |||
| [25.0,52.6) | 29.000 | 87.000 | 0.137 |
| [52.6,92.0] | 19.000 | 32.000 | |
| [25.0,52.6) | 0.604 | 0.731 | |
| [52.6,92.0] | 0.396 | 0.269 | |
| Singletons | |||
| [ 0.00, 8.47) | 29.000 | 87.000 | |
| [ 8.47,17.00] | 19.000 | 32.000 | |
| [ 0.00, 8.47) | 0.604 | 0.731 | |
| [ 8.47,17.00] | 0.396 | 0.269 | |
| term | estimate | p.value |
|---|---|---|
| (Intercept) | 3.151 | 0.303 |
| fra_fr3 | 0.078 | 0.088 |
| spl_fr1 | 0.050 | 0.063 |
| spl_fr4 | 0.291 | 0.158 |
| sto_fr3 | -0.159 | 0.128 |
| sto_fr4 | 0.597 | 0.019 |
| nfr_fr1 | 0.041 | 0.04 |
| nfr_fr4 | 0.324 | 0.114 |
| syn_fr1 | -0.002 | 0.005 |
| syn_fr2 | -0.011 | 0.017 |
| syn_fr3 | 0.017 | 0.048 |
| H | AUC | KS | TP | FP | TN | FN | |
|---|---|---|---|---|---|---|---|
| scores | 0.223 | 0.716 | 0.408 | 10 | 14 | 48 | 11 |
##
## Classification tree:
## rpart(formula = fml, data = lrn)
##
## Variables actually used in tree construction:
## [1] nsy_fr2 spl_fr3 sto_fr1 syn_fr3 syn_fr4
##
## Root node error: 27/84 = 0.32142857
##
## n= 84
##
## CP nsplit rel error xerror xstd
## 1 0.185185185 0 1.00000000 1.0000000 0.15853162
## 2 0.074074074 1 0.81481481 1.2222222 0.16578249
## 3 0.037037037 2 0.74074074 1.2592593 0.16661767
## 4 0.010000000 6 0.59259259 1.2962963 0.16735113
| H | AUC | KS | TP | FP | TN | FN | |
|---|---|---|---|---|---|---|---|
| scores | 0.03 | 0.52 | 0.114 | 20 | 52 | 10 | 1 |
| H | AUC | KS | TP | FP | TN | FN | |
|---|---|---|---|---|---|---|---|
| V1 | 0 | 0.5 | 0 | 0 | 0 | 62 | 21 |
| H | AUC | KS | TP | FP | TN | FN | |
|---|---|---|---|---|---|---|---|
| scores | 0.231 | 0.706 | 0.33 | 1 | 0 | 62 | 20 |
| Number of LoF | Affected | Control | Fisher |
|---|---|---|---|
| Grouping Method: Frequency | |||
| Rare variants | |||
| [ 650,1494) | 28.000 | 56.000 | 0.232 |
| [1494,2728] | 20.000 | 63.000 | |
| [ 650,1494) | 0.583 | 0.471 | |
| [1494,2728] | 0.417 | 0.529 | |
| Singletons | |||
| [ 62,175) | 25.000 | 60.000 | 0.866 |
| [175,258] | 23.000 | 59.000 | |
| [ 62,175) | 0.521 | 0.504 | |
| [175,258] | 0.479 | 0.496 | |
| Grouping Method: Presence versus Absence | |||
| Rare variants | |||
| 0 | 0.000 | 0.000 | 1 |
| [ 1,2728] | 48.000 | 119.000 | |
| 0 | 0.000 | 0.000 | |
| [ 1,2728] | 1.000 | 1.000 | |
| Singletons | |||
| 0 | 0.000 | 0.000 | |
| [ 1,2728] | 48.000 | 119.000 | |
| 0 | 0.000 | 0.000 | |
| [ 1,2728] | 1.000 | 1.000 | |
| Grouping Method: Kmeans | |||
| Rare variants | |||
| [ 650,1481) | 28.000 | 54.000 | 0.171 |
| [1481,2728] | 20.000 | 65.000 | |
| [ 650,1481) | 0.583 | 0.454 | |
| [1481,2728] | 0.417 | 0.546 | |
| Singletons | |||
| [ 62,146) | 9.000 | 33.000 | 0.245 |
| [146,258] | 39.000 | 86.000 | |
| [ 62,146) | 0.188 | 0.277 | |
| [146,258] | 0.812 | 0.723 | |
| term | estimate | p.value |
|---|---|---|
| (Intercept) | -7.029 | 0.005 |
| utr5_fr1 | -0.004 | 0.032 |
| utr5_fr2 | 0.058 | 0.034 |
| utr3_fr3 | -0.013 | 0.007 |
| ncRNA_fr1 | 0.003 | 0.145 |
| ncRNA_fr3 | 0.028 | 0.002 |
| ncRNA_fr4 | 0.152 | 0.064 |
| miRNA_fr3 | 0.972 | 0.02 |
| miRNA_fr4 | -3.421 | 0.016 |
| bnd_fr1 | 0.001 | 0.053 |
| bnd_fr2 | -0.009 | 0.031 |
| reg_fr1 | -0.027 | 0.126 |
| reg_fr3 | 0.132 | 0.076 |
| H | AUC | KS | TP | FP | TN | FN | |
|---|---|---|---|---|---|---|---|
| scores | 0.108 | 0.627 | 0.234 | 7 | 12 | 50 | 14 |
##
## Classification tree:
## rpart(formula = fml, data = lrn)
##
## Variables actually used in tree construction:
## [1] bnd_fr1 ncRNA_fr3 utr3_fr3
##
## Root node error: 27/84 = 0.32142857
##
## n= 84
##
## CP nsplit rel error xerror xstd
## 1 0.22222222 0 1.00000000 1.00000000 0.15853162
## 2 0.11111111 2 0.55555556 0.70370370 0.14201364
## 3 0.01000000 4 0.33333333 0.74074074 0.14457779
| H | AUC | KS | TP | FP | TN | FN | |
|---|---|---|---|---|---|---|---|
| scores | 0.299 | 0.764 | 0.412 | 10 | 4 | 58 | 11 |
| H | AUC | KS | TP | FP | TN | FN | |
|---|---|---|---|---|---|---|---|
| V1 | 0 | 0.5 | 0 | 0 | 0 | 62 | 21 |
| H | AUC | KS | TP | FP | TN | FN | |
|---|---|---|---|---|---|---|---|
| scores | 0.285 | 0.752 | 0.441 | 2 | 2 | 60 | 19 |